A study just released in Science Magazine claiming that farmed salmon poses risks of cancer is already contested by French scientists who find its methods and figures debatable. I've heard one argument that strikes me as evident: this study makes statistical claims on samples as small as three fishes bought on a local market (incidentally, this is how they assert that Northern European fish is more polluted while, as I understand it, the European samples are the smallest hence prone to statistical irrelevance), while measures done by European agencies are made on much bigger samples and show levels of pollutants below the WHO acceptable levels. The U.S. FDA finds this study over-alarming.
However, it's always good to make people aware that between an animal which feeds itself naturally and one that is forced-fed to grow as fa(s)t as possible, there are differences likely to cause health problems. As for the fish, this will be true as long as the sea is big enough to dilute all the junk we throw in it, of course.
Note: Science Mag's site is apparently down at the moment and since Wired has this nasty habit (widespread amongst journalists) of not linking to others' sites, I haven't seen the study itself.